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#!/bin/bash #PBS -P PROJECT #PBS -l select=1:ncpus=4:mem=4gb #PBS -l walltime=0:10:00 module load singularity/2.6.1 #Change into the directory you executed qsub from cd "$PBS_O_WORKDIR" #Run the singularity image, which contains the program Trinity #The dataset "reads.fq.gz" should be in this directory, #This will create persistent output in a folder called "trinity_out_dir" singularity exec Singularity.trinity.build Trinity --seqType fq --single `pwd`/reads.fq.gz --max_memory 4G --CPU $NCPUS --output `pwd`/trinity_out_dir |
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